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Encountered several times when returned values contain non-escaped \n. This is interpreted as a new row and breaks the table reading.
host="https://www.ensembl.org:443/biomart/martservice?"query="<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= 'biomaRt' formatter = 'TSV'><Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'hgnc_symbol'/><Attribute name = 'go_id'/><Attribute name = 'name_1006'/><Attribute name = 'definition_1006'/><Filter name = \"ensembl_gene_id\" value = \"ENSG00000100036\" /></Dataset></Query>"res<-httr::POST(url=host, body=list(query=query),
httr::set_cookies(.cookies= c(redirect_mirror="no")))
con= textConnection(httr::content(res))
result= read.table(con, sep=",", header=TRUE, quote="\"", comment.char="", as.is=TRUE, check.names=TRUE, allowEscapes=TRUE)
Solution: The HTML version of the output seems to handle this correctly. This is larger and more complex to parse, but could be used as a backup if TSV is failing.
The text was updated successfully, but these errors were encountered:
Example: https://support.bioconductor.org/p/121356/
Encountered several times when returned values contain non-escaped
\n
. This is interpreted as a new row and breaks the table reading.Solution: The HTML version of the output seems to handle this correctly. This is larger and more complex to parse, but could be used as a backup if TSV is failing.
The text was updated successfully, but these errors were encountered: